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How would one bulk export annotations to CSV (Read 3642 times)
Jul 26th, 2016 at 3:20am

AnthonyJumelles   Offline
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I was hoping that there would be some way to export all of the annotations in a GenBank file but it seems that you'd have to individually select each one, pick a name, and then select CSV to export and as I have several thousand, I'd rather prefer not to waste the time.

Is there any way to export all annotations automatically as either one file or separate? If not, are there any programs that do so?
 

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Reply #1 - Jul 27th, 2016 at 5:24pm

Olga Golosova   Offline
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Hello, Anthony!

In short, you may use the UGENE Workflow Designer to do it.

You should:
1) Create a workflow "Read Annotations" > "Write annotations".
2) Modify values of the "Write annotations" parameters as follows:
  • "Existing file": "Append"
  • "Document format": "csv"
  • "Output file": any file name

This scenario will be described in detail (with screenshots) tomorrow in our Facebook group (https://www.facebook.com/groups/ugene/).
 
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Reply #2 - Jul 27th, 2016 at 8:25pm

AnthonyJumelles   Offline
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Appreciate it, would have never thought to look there! I'll be sure to join too.
 
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